Change transformer vector group

Transformer nameplate vector group is YNd1. However, the nature of connection on both its primary and secondary side is such that:
Generator phase A = Transformer phase c
Generator phase B = Transformer phase b
Generator phase C = Transformer phase a

Also, on transformer HV (secondary connected to grid),
Transformer phase A = Grid phase C
Transformer phase B = Grid phase B
Transformer phase C = Grid phase A

The questions are:

1. How does this affect the vector group (YNd1) of the transformer? Will it be changed to YNd11?
2. Will it make any difference as far as the vector group is concerned if instead of phase A and C, phase B and C were swapped on both ends of the transformer?
3. The transformer protection relay is configured for YNd1 group, and it is reading negative phase sequence current (ACB instead of ABC). Changing the vector group configuration will solve the problem?
4. Relay is used for differential protection (percentage differential) of the transformer.
Will this negative phase sequence affect normal operation of the transformer in any way?

1. How does this affect the vector group (YNd1) of the transformer? Will it be changed to YNd11?

Yes, the name plate vector group of a transformer is only valid for a standard phase rotation ABC. for a phase rotation ACB the apparent vector group will be YNd11.

2. Will it make any difference as far as the vector group is concerned if instead of phase A and C, phase B and C were swapped on both ends of the transformer?

No, by swapping any two phases the rotation becomes no standard and the apparent vector group will become YNd1

3. The transformer protection relay is configured for YNd1 group, and it is reading negative phase sequence current (ACB instead of ABC). Changing the vector group configuration will solve the problem?

I think the way the relay is configured at the moment will give you problems, if I'm correct you should be able to see differential current when the transformer is loaded, and it is likely to trip on the first through fault (can you confirm this). To resolve this issue you have two options.
i) Set the vector group to YNd11 in the relay, this will remove the differential current but will mean the relays see's 100% NPS current and 0% PPS current, this may give you problem if you have any NPS elements enabled in the relay ( inter turn fault detection, directional elements etc)
ii)Set the vector group to YNd1 and the phase rotation setting to non standard ACB this will get rid of the NPS currents and the differential current, so this is probably the best solution.

4. Relay is used for differential protection (percentage differential) of the transformer.
Will this negative phase sequence affect normal operation of the transformer in any way?

No, there will be no problem with the transformer itself just the relay protecting it.

As i said previously if I'm understanding the problem correctly, you should be able to see differential current at the moment when the transformer is loaded, is this correct?